MR microscopy of the lung in small animals is particularly challenging because of the low spin density, short T2 and T2*, and cardiac and breathing motion. Previous work demonstrated 2D solutions to these challenges [--- Pict Graphic Goes Here ---] but extrapolation to 3D has not been possible because of the greater degree of motion control required, limits in signal-to-noise, and long imaging times required for most 3D sequences. This work describes a new MR-compatible ventilator and its application to 3D projection encoding using both 1H and 3He to allow 3D microscopy of the lungs at resolution of 0.01 mm3 at selected phases of the breathing cycle. The ventilator permits control of lung volumes, delivery of test gasses, and breathing motion not previously possible.